Comments (7)
Does the command line version of curl work for you?
curl -O "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/hg19/latest/PhyloCSF+0.bw"
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@hussius As @ghuls mentioned, if you can get curl
on the command line to work then pyBigWig should work too.
I should note that I've been meaning to have open()
default to ignoring SSL certificate issues, since I don't expect regular end users (e.g., all the deepTools users) to have to deal with that.
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It does work for me on the command line.
130-229-4-255-dhcp:~ mikaelhuss$ curl -O "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/hg19/latest/PhyloCSF+0.bw"
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 3019M 0 4622k 0 0 1189k 0 0:43:19 0:00:03 0:43:16 1189k
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My only guess is that whichever libcurl pyBigWig is getting linked against is using a different CAPATH. I really just need to adjust pyBigWig to ignore such things by default. In the interim, you can add the following to libBigWig/io.c
after line 234:
if(curl_easy_setopt(URL->x.curl, CURLOPT_SSL_VERIFYPEER, 0) != CURLE_OK) {
fprintf(stderr, "[urlOpen] Couldn't set CURLOPT_SSL_VERIFYPEER to 0!\n");
goto error;
}
That won't solve the root problem, but it'll probably get things running.
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Go figure - it works for me now in a fresh conda environment. I did not try the @dpryan79 addition because with my conda-installed package on Mac, pyBigWig.__file__
points to a .so file and I can't find any C source files. Cheers!
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Ah, I'm not sure conda was using the system-installed certificates (there have also been on-going issues with libcurl on OSX in conda, I used to have a separate curl inside bioconda for this reason). Anyway, I'll leave this open as a reminder to myself to just have these sorts of errors ignored.
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Starting in version 0.3.5 certificate issues should generally be ignored. I considered making certificate checks optional, but I suspect no one would ever actually bother to use that and adding it in would be a bit annoying, so I'll hold off unless someone explicitly asks for it.
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Related Issues (20)
- RuntimeError: Invalid interval bounds
- Document performance considerations? HOT 4
- Cannot add entries of value type int, but only float HOT 2
- support for osx-arm64 HOT 2
- numpy support broken in 0.3.18? HOT 1
- Create a BedGraph file using addEntries() throws segmentation fault HOT 2
- library import error HOT 4
- pyBigWig fails to find numpy installation when installing from PyPI HOT 5
- Writing a nan value should leave a gap HOT 7
- Can't enforce numpy features when pyBigWig is used as a dependency in downstream package HOT 5
- pip installation broken HOT 4
- Installing through pip not working HOT 9
- addHeader does not support multiple calls HOT 1
- Support for python >=3.11 HOT 1
- Issue Downloading pyBigWig HOT 1
- Simple patch to resolve conflict with roundup() macro
- Stats Sum Not Working as Expected
- 'zsh: segmentation fault ' HOT 1
- Out of memory listing entries on one human chromosome on a machine with 300 GB ram and 165 GB BigBed file HOT 1
- pyBigWig.entries() should return empty array, not None when no entries are found
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